Puerto Rico can be played by three to five players, although an official two player variant also exists. There is an official expansion which adds new buildings that can be swapped in for or used along with those in the original game. In February 2004, Andreas Seyfarth released a separate card game called San Juan based on Puerto Rico and published by the same companies. Puerto Rico is one of the highest rated games on BoardGameGeek.

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Each player uses a separate small board with spaces for city buildings, plantations, and resources. Shared between the players are three ships, a trading house, and a supply of resources and doubloons (money).

The resource cycle of the game is that players grow crops which they exchange for points or doubloons. Doubloons can then be used to buy buildings, which allow players to produce more crops or give them other abilities. Buildings and plantations do not work unless they are manned by colonists.

During each round, players take turns selecting a role card from those on the table (such as "Trader" or "Builder"). When a role is chosen, every player gets to take the action appropriate to that role. The player that selected the role also receives a small privilege for doing so - for example, choosing the "Builder" role allows all players to construct a building, but the player who chose the role may do so at a discount on that turn. Unused roles gain a doubloon bonus at the end of each turn, so the next player who chooses that role gets to keep any doubloon bonus associated with it. This encourages players to make use of all the roles throughout a typical course of a game.

Puerto Rico uses a variable phase order mechanic, where a "governor" token is passed clockwise to the next player at the conclusion of a turn. The player with the token begins the round by choosing a role and taking the first action.

Players earn victory points for owning buildings, for shipping goods, and for manned "large buildings." Each player's accumulated shipping chips are kept face down and come in denominations of one or five. This prevents other players from being able to determine the exact score of another player. Goods and doubloons are placed in clear view of other players and the totals of each can always be requested by a player. As the game enters its later stages, the unknown quantity of shipping tokens and its denominations require players to consider their options before choosing a role that can end the game.

Mayor is selected and there are not enough colonists to refill the colonist ship with the appropriate amount.

Captain is selected and the last VP chip is given to a player. (Additional chips are to be used once the supply is exhausted)

Builder is selected and at least one player has built their 12th city space.

In each case, players finish the current round before the game ends.

A player's total score is calculated by adding the number on each of their victory chips, plus the building value of all of their buildings. Manned large buildings award bonus points based on various game conditions (such as the Fortress, which gives one victory point for every three colonists on the player board, or the City Hall, which awards a point for every small or large violet building owned by the player).

The winner is the player with the most victory points. In the event of a tie, the player with the most total goods plus doubloons is given the tie-breaker. If a tie still exists between players, those players tie.

There are two primary strategies used in Puerto Rico, corresponding to the two means of earning victory points. One route is to go with higher goods production, to send the goods back to the homeland for points. Corn is produced free and indigo has low investment cost. Therefore, these are commonly mass-produced. However, doubloons are harder to acquire. The other route is producing smaller cash crops (tobacco and coffee) and buying more buildings. Expensive buildings can give a player 10 victory points, but fewer goods are likely to get moved to the homeland. However, in filling all the building spaces, a player can finish the game quickly and keep others from getting more shipment victory points.

In January 2004, Alea released an expansion to Puerto Rico. The addition consists of 14 new buildings that may be used alongside or instead of the original 17.

A second expansion was under development, but it was later announced that it was canceled. Instead, an expansion is included in the Alea 10th anniversary 'treasure chest' released in 2009, which contains expansions for a number of different Alea games. The Puerto Rico expansions included consist of the original expansion as well as a small expansion of several new buildings and red 'nobleman' colonists, which interact with the new buildings. An English language translation was released at the end of 2009 by Rio Grande Games.

A playable online version is available, and up to June 2014, over 260,000 games have been played this way.[3] An iPad version was launched in August, 2011.[4]

The following changes may be made to the official rules in order to create a more balanced game and one which gives each player an equal chance of winning:

The prices of the Factory and University buildings should be swapped so that the Factory costs 8 doubloons and the University costs 7 doubloons. The designer Andreas Seyfarth has said he would make this change if he were creating the game today.[5]

Any players that start with a corn plantation should start with 1 doubloon less than the players that start with an indigo plantation.[6]